Mercurial > repos > galaxyp > msconvert
changeset 0:10f4a0356342
Uploaded
| author | galaxyp |
|---|---|
| date | Wed, 19 Dec 2012 00:10:08 -0500 |
| parents | |
| children | 861e3f0c2bb6 |
| files | LICENSE README.md README_GALAXYP.md README_REPO.md msconvert.xml.template msconvert2.xml msconvert2_raw.xml msconvert3.xml msconvert3_raw.xml msconvert_raw_wrapper.py msconvert_subset.xml msconvert_wrapper.py update.sh update_repo.sh version |
| diffstat | 15 files changed, 2572 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,47 @@ +# msconvert + +This repository contains Galaxy tool wrappers for msconvert, part of +the ProteoWizard (http://proteowizard.sourceforge.net/) package. + +# Installing + +Due to potential difficulties installing ProteoWizard with vendor +library support, tools for interacting with vendor types are seperated +out into their own wrappers. Galaxy is generally deployed under Linux, +but vendor support in ProteoWizard requires .NET 4.0. There are at +least two ways to get this to work: + + * Galaxy jobs may be configured to submit to a Windows host with + ProteoWizard installed using the + LWR. http://wiki.g2.bx.psu.edu/Admin/Config/LWR + + * ProteoWizard can be installed under Wine. Guidance on how to set + this up and package such environments for cloud deployments can be + found here: https://github.com/jmchilton/proteomics-wine-env + +Wrappers for both msconvert version 2 and version 3+ are provided +because version 3+ of msconvert with vendor library support requires +.NET 4.0 and this may difficult or impossible under Wine in Linux with +all but the most recent versions of Wine (1.4+). +# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_GALAXYP.md Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,22 @@ +# Obtaining Tools + +Repositories for all Galaxy-P tools can be found at +https:/bitbucket.org/galaxyp/. + +# Contact + +Please send suggestions for improvements and bug reports to +jmchilton@gmail.com. + +# License + +All Galaxy-P tools are licensed under the Apache License Version 2.0 +unless otherwise documented. + +# Tool Versioning + +Galaxy-P tools will have versions of the form X.Y.Z. Versions +differing only after the second decimal should be completely +compatible with each other. Breaking changes should result in an +increment of the number before and/or after the first decimal. All +tools of version less than 1.0.0 should be considered beta.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README_REPO.md Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,25 @@ +# msconvert + +This repository contains Galaxy tool wrappers for msconvert, part of +the ProteoWizard (http://proteowizard.sourceforge.net/) package. + +# Installing + +Due to potential difficulties installing ProteoWizard with vendor +library support, tools for interacting with vendor types are seperated +out into their own wrappers. Galaxy is generally deployed under Linux, +but vendor support in ProteoWizard requires .NET 4.0. There are at +least two ways to get this to work: + + * Galaxy jobs may be configured to submit to a Windows host with + ProteoWizard installed using the + LWR. http://wiki.g2.bx.psu.edu/Admin/Config/LWR + + * ProteoWizard can be installed under Wine. Guidance on how to set + this up and package such environments for cloud deployments can be + found here: https://github.com/jmchilton/proteomics-wine-env + +Wrappers for both msconvert version 2 and version 3+ are provided +because version 3+ of msconvert with vendor library support requires +.NET 4.0 and this may difficult or impossible under Wine in Linux with +all but the most recent versions of Wine (1.4+).
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert.xml.template Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,386 @@ +<tool id="msconvert$VERSION$DESCRIPTION" name="msconvert$VERSION$DESCRIPTION" version="0.1.0"> + <!-- BEGIN_VERSION_RAW --> + <description>Convert and filter a Thermo Finnigan RAW file</description> + <!-- END_VERSION_RAW --> + <!-- BEGIN_VERSION_DEFAULT --> + <description>Convert and filter a mass spec peak list</description> + <!-- END_VERSION_DEFAULT --> + + <command interpreter="python"> + msconvert_wrapper.py + --input=${input} + #if hasattr($input, 'display_name') + --input_name='${input.display_name}' + #end if + --output=${output} + ## BEGIN_VERSION_DEFAULT + --fromextension=${input.ext} + ## END_VERSION_DEFAULT + + ## BEGIN_VERSION_RAW + --fromextension=RAW + ## END_VERSION_RAW + + --toextension=${output_type} + + #if $settings.settingsType == "full" + --binaryencoding=${settings.binary_encoding} + --mzencoding=${settings.mz_encoding} + --intensityencoding=${settings.intensity_encoding} + --zlib=${settings.zlib} + #end if + + #if $filtering.filtering_use + + #if $filtering.precursor_recalculation.value + --filter "precursorRecalculation" + #end if + + #if $filtering.peak_picking.pick_peaks + --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" + #end if + + #if str($filtering.activation) != "false" + --filter "activation $filtering.activation" + #end if + + #if len($filtering.indices) > 0 + --filter "index + #for $index in $filtering.indices + [${index.from},${index.to}] + #end for + " + #end if + + #if len($filtering.scan_numbers) > 0 + --filter "scanNumber + #for $scan_number in $filtering.scan_numbers + [${scan_number.from},${scan_number.to}] + #end for + " + #end if + + #for threshold_entry in $filtering.threshold_repeat + --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation" + #end for + + + #if $filtering.strip_it.value + --filter "stripIT" + #end if + + #if $filtering.filter_mz_windows.do_filter + --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" + #end if + + + #if $filtering.filter_ms_levels.do_filter + --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "default" + --filter "ETDFilter" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" + --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units" + #end if + + ## BEGIN_VERSION_3 + + #if $filtering.precursor_refine.value + --filter "precursorRefine" + #end if + + #if $filtering.ms2denoise.denoise + --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax" + #end if + + #if str($filtering.ms2deisotope) == "true" + --filter "MS2Deisotope" + #end if + + #if str($filtering.polarity) != "false" + --filter "polarity $filtering.polarity" + #end if + + #if str($filtering.analyzer) != "false" + --filter "analyzer $filtering.analyzer" + #end if + + ## END_VERSION_3 + + #end if + + </command> + + <inputs> + <!-- BEGIN_VERSION_RAW --> + <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/> + <!-- END_VERSION_RAW --> + + <!-- BEGIN_VERSION_DEFAULT --> + <conditional name="type"> + <param name="input_type" type="select" label="Input Type"> + <option value="mzml">mzML</option> + <option value="mzxml">mzXML</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <when value="mzml"> + <param format="mzml" name="input" type="data" label="Input mzML"/> + </when> + <when value="mzxml"> + <param format="mzxml" name="input" type="data" label="Input mzXML"/> + </when> + <when value="mgf"> + <param format="mgf" name="input" type="data" label="Input mgf"/> + </when> + <when value="ms2"> + <param format="ms2" name="input" type="data" label="Input ms2"/> + </when> + </conditional> + <!-- END_VERSION_DEFAULT --> + <param name="output_type" type="select" label="Output Type"> + <option value="mzML">mzML (indexed)</option> + <option value="unindexed_mzML">mzML (unindexed)</option> + <option value="mzXML">mzXML (indexed)</option> + <option value="unindexed_mzXML">mzXML (unindexed)</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <conditional name="filtering"> + <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> + <!-- BEGIN_VERSION_3 --> + <param type="boolean" name="precursor_refine" label="Refine Precursor?" /> + <!-- END_VERSION_3 --> + + + <conditional name="peak_picking"> + <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> + <option value="1">MS1 Only (1)</option> + <option value="2">MS2 Only (2)</option> + <option value="2-">MS2 and on (2-)</option> + <option value="1-">All Levels (1-)</option> + </param> + <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> + </when> + </conditional> + + <repeat name="threshold_repeat" title="Filter by Threshold"> + <conditional name="threshold"> + <param type="select" label="Specify threshold on" name="threshold_type" help=""> + <option value="count">Peak count</option> + <option value="count-after-ties">Peak count (after ties)</option> + <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z --> + <option value="bpi-relative">Percent of base peak intensity</option> + <option value="tic-relative">Percent of total ion current</option> + <option value="tic-fraction">Aggregate percent of total ion current</option> + </param> + <when value="count"> + <param type="integer" name="value" label="Number of peaks to keep" value="100" /> + </when> + <when value="count-after-ties"> + <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" /> + </when> + <when value="absolute"> + <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" /> + </when> + <when value="bpi-relative"> + <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2" + /> + </when> + <when value="tic-relative"> + <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2" + /> + </when> + <when value="tic-fraction"> + <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" /> + </when> + </conditional> + <param type="select" label="Keep" name="orientation"> + <option value="most-intense">Most intense peaks</option> + <option value="least-intense">Least intense peaks</option> + </param> + </repeat> + + + <param name="activation" type="select" label="Filter by Activation"> + <option value="false" selected="true">no</option> + <option value="ETD">ETD</option> + <option value="CID">CID</option> + <option value="SA">SA</option> + <option value="HCD">HCD</option> + <!-- BEGIN_VERSION_3 --> + <option>BIRD</option> + <option>ECD</option> + <option>IRMPD</option> + <option>PD</option> + <option>PSD</option> + <option>PQD</option> + <option>SID</option> + <option>SORI</option> + <!-- END_VERSION_3 --> + </param> + + <repeat name="indices" title="Filter Scan Indices"> + <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> + </repeat> + + <repeat name="scan_numbers" title="Filter Scan Numbers"> + <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> + </repeat> + + <conditional name="filter_mz_windows"> + <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> + <when value="false" /> + <when value="true"> + <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> + <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> + </when> + </conditional> + + <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> + + <conditional name="filter_ms_levels"> + <param name="do_filter" type="boolean" label="Filter MS Levels" /> + <when value="false" /> + <when value="true"> + <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> + </when> + </conditional> + + <conditional name="etd_filtering"> + <param name="do_etd_filtering" type="select" label="ETD Filtering"> + <option value="none" selected="true">none</option> + <option value="default">yes (with default options)</option> + <option value="advanced">yes (show advanced options) </option> + </param> + <when value="none" /> + <when value="default" /> + <when value="advanced"> + <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> + </param> + <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> + <option value="MZ" selected="true">mz</option> + <option value="PPM">ppm</option> + </param> + <param name="remove_precursor" type="select" label="ETD Remove Precursor"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="blanket_removal" type="select" label="ETD Blanket Removal"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + </when> + </conditional> + + + <!-- BEGIN_VERSION_3 --> + <conditional name="ms2denoise"> + <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" /> + <when value="true"> + <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" /> + <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" /> + <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" /> + </when> + <when value="false" /> + </conditional> + <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" /> + + <param name="polarity" type="select" label="Filter by Polarity"> + <option value="false" selected="true">no</option> + <option value="positive">positive</option> + <option value="negative">negative</option> + </param> + + <param name="analyzer" type="select" label="Filter by Analyzer"> + <option value="false" selected="true">no</option> + <option value="quad">quad</option> + <option value="orbi">orbi</option> + <option value="FT">FT</option> + <option value="IT">IT</option> + <option value="TOF">TOF</option> + </param> + <!-- END_VERSION_3 --> + </when> + </conditional> + + <conditional name="settings"> + <param name="settingsType" type="select" label="Advanced Settings" help=""> + <option value="default">Use Defaults</option> + <option value="full">Full Parameter List</option> + </param> + <when value="default" /> + <when value="full"> + <param type="select" name="binary_encoding" label="Binary Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="mz_encoding" label="m/z Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> + <option value="64">64</option> + <option value="32" selected="true">32</option> + </param> + <param type="boolean" name="zlib" label="Use zlib"> + </param> + </when> + </conditional> + + + </inputs> + <outputs> + <data format="mzml" name="output"> + <change_format> + <when input="output_type" value="mzXML" format="mzxml" /> + <when input="output_type" value="unindexed_mzXML" format="mzxml" /> + <when input="output_type" value="ms2" format="ms2" /> + <when input="output_type" value="mgf" format="mgf" /> + </change_format> + </data> + </outputs> + + <requirements> + <requirement type="package">proteowizard</requirement> + </requirements> + + <help> +**What it does** + +Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. + +You can view the original documentation here_. + +.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html + +------ + +**Citation** + +For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert2.xml Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,314 @@ +<tool id="msconvert2" name="msconvert2" version="0.1.0"> + <!-- BEGIN_VERSION_DEFAULT --> + <description>Convert and filter a mass spec peak list</description> + <!-- END_VERSION_DEFAULT --> + + <command interpreter="python"> + msconvert_wrapper.py + --input=${input} + #if hasattr($input, 'display_name') + --input_name='${input.display_name}' + #end if + --output=${output} + ## BEGIN_VERSION_DEFAULT + --fromextension=${input.ext} + ## END_VERSION_DEFAULT + + + --toextension=${output_type} + + #if $settings.settingsType == "full" + --binaryencoding=${settings.binary_encoding} + --mzencoding=${settings.mz_encoding} + --intensityencoding=${settings.intensity_encoding} + --zlib=${settings.zlib} + #end if + + #if $filtering.filtering_use + + #if $filtering.precursor_recalculation.value + --filter "precursorRecalculation" + #end if + + #if $filtering.peak_picking.pick_peaks + --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" + #end if + + #if str($filtering.activation) != "false" + --filter "activation $filtering.activation" + #end if + + #if len($filtering.indices) > 0 + --filter "index + #for $index in $filtering.indices + [${index.from},${index.to}] + #end for + " + #end if + + #if len($filtering.scan_numbers) > 0 + --filter "scanNumber + #for $scan_number in $filtering.scan_numbers + [${scan_number.from},${scan_number.to}] + #end for + " + #end if + + #for threshold_entry in $filtering.threshold_repeat + --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation" + #end for + + + #if $filtering.strip_it.value + --filter "stripIT" + #end if + + #if $filtering.filter_mz_windows.do_filter + --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" + #end if + + + #if $filtering.filter_ms_levels.do_filter + --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "default" + --filter "ETDFilter" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" + --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units" + #end if + + + #end if + + </command> + + <inputs> + + <!-- BEGIN_VERSION_DEFAULT --> + <conditional name="type"> + <param name="input_type" type="select" label="Input Type"> + <option value="mzml">mzML</option> + <option value="mzxml">mzXML</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <when value="mzml"> + <param format="mzml" name="input" type="data" label="Input mzML"/> + </when> + <when value="mzxml"> + <param format="mzxml" name="input" type="data" label="Input mzXML"/> + </when> + <when value="mgf"> + <param format="mgf" name="input" type="data" label="Input mgf"/> + </when> + <when value="ms2"> + <param format="ms2" name="input" type="data" label="Input ms2"/> + </when> + </conditional> + <!-- END_VERSION_DEFAULT --> + <param name="output_type" type="select" label="Output Type"> + <option value="mzML">mzML (indexed)</option> + <option value="unindexed_mzML">mzML (unindexed)</option> + <option value="mzXML">mzXML (indexed)</option> + <option value="unindexed_mzXML">mzXML (unindexed)</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <conditional name="filtering"> + <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> + + + <conditional name="peak_picking"> + <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> + <option value="1">MS1 Only (1)</option> + <option value="2">MS2 Only (2)</option> + <option value="2-">MS2 and on (2-)</option> + <option value="1-">All Levels (1-)</option> + </param> + <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> + </when> + </conditional> + + <repeat name="threshold_repeat" title="Filter by Threshold"> + <conditional name="threshold"> + <param type="select" label="Specify threshold on" name="threshold_type" help=""> + <option value="count">Peak count</option> + <option value="count-after-ties">Peak count (after ties)</option> + <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z --> + <option value="bpi-relative">Percent of base peak intensity</option> + <option value="tic-relative">Percent of total ion current</option> + <option value="tic-fraction">Aggregate percent of total ion current</option> + </param> + <when value="count"> + <param type="integer" name="value" label="Number of peaks to keep" value="100" /> + </when> + <when value="count-after-ties"> + <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" /> + </when> + <when value="absolute"> + <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" /> + </when> + <when value="bpi-relative"> + <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2" + /> + </when> + <when value="tic-relative"> + <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2" + /> + </when> + <when value="tic-fraction"> + <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" /> + </when> + </conditional> + <param type="select" label="Keep" name="orientation"> + <option value="most-intense">Most intense peaks</option> + <option value="least-intense">Least intense peaks</option> + </param> + </repeat> + + + <param name="activation" type="select" label="Filter by Activation"> + <option value="false" selected="true">no</option> + <option value="ETD">ETD</option> + <option value="CID">CID</option> + <option value="SA">SA</option> + <option value="HCD">HCD</option> + </param> + + <repeat name="indices" title="Filter Scan Indices"> + <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> + </repeat> + + <repeat name="scan_numbers" title="Filter Scan Numbers"> + <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> + </repeat> + + <conditional name="filter_mz_windows"> + <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> + <when value="false" /> + <when value="true"> + <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> + <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> + </when> + </conditional> + + <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> + + <conditional name="filter_ms_levels"> + <param name="do_filter" type="boolean" label="Filter MS Levels" /> + <when value="false" /> + <when value="true"> + <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> + </when> + </conditional> + + <conditional name="etd_filtering"> + <param name="do_etd_filtering" type="select" label="ETD Filtering"> + <option value="none" selected="true">none</option> + <option value="default">yes (with default options)</option> + <option value="advanced">yes (show advanced options) </option> + </param> + <when value="none" /> + <when value="default" /> + <when value="advanced"> + <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> + </param> + <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> + <option value="MZ" selected="true">mz</option> + <option value="PPM">ppm</option> + </param> + <param name="remove_precursor" type="select" label="ETD Remove Precursor"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="blanket_removal" type="select" label="ETD Blanket Removal"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + </when> + </conditional> + + + </when> + </conditional> + + <conditional name="settings"> + <param name="settingsType" type="select" label="Advanced Settings" help=""> + <option value="default">Use Defaults</option> + <option value="full">Full Parameter List</option> + </param> + <when value="default" /> + <when value="full"> + <param type="select" name="binary_encoding" label="Binary Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="mz_encoding" label="m/z Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> + <option value="64">64</option> + <option value="32" selected="true">32</option> + </param> + <param type="boolean" name="zlib" label="Use zlib"> + </param> + </when> + </conditional> + + + </inputs> + <outputs> + <data format="mzml" name="output"> + <change_format> + <when input="output_type" value="mzXML" format="mzxml" /> + <when input="output_type" value="unindexed_mzXML" format="mzxml" /> + <when input="output_type" value="ms2" format="ms2" /> + <when input="output_type" value="mgf" format="mgf" /> + </change_format> + </data> + </outputs> + + <requirements> + <requirement type="package">proteowizard</requirement> + </requirements> + + <help> +**What it does** + +Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. + +You can view the original documentation here_. + +.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html + +------ + +**Citation** + +For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert2_raw.xml Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,295 @@ +<tool id="msconvert2_raw" name="msconvert2_raw" version="0.1.0"> + <!-- BEGIN_VERSION_RAW --> + <description>Convert and filter a Thermo Finnigan RAW file</description> + <!-- END_VERSION_RAW --> + + <command interpreter="python"> + msconvert_wrapper.py + --input=${input} + #if hasattr($input, 'display_name') + --input_name='${input.display_name}' + #end if + --output=${output} + + ## BEGIN_VERSION_RAW + --fromextension=RAW + ## END_VERSION_RAW + + --toextension=${output_type} + + #if $settings.settingsType == "full" + --binaryencoding=${settings.binary_encoding} + --mzencoding=${settings.mz_encoding} + --intensityencoding=${settings.intensity_encoding} + --zlib=${settings.zlib} + #end if + + #if $filtering.filtering_use + + #if $filtering.precursor_recalculation.value + --filter "precursorRecalculation" + #end if + + #if $filtering.peak_picking.pick_peaks + --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" + #end if + + #if str($filtering.activation) != "false" + --filter "activation $filtering.activation" + #end if + + #if len($filtering.indices) > 0 + --filter "index + #for $index in $filtering.indices + [${index.from},${index.to}] + #end for + " + #end if + + #if len($filtering.scan_numbers) > 0 + --filter "scanNumber + #for $scan_number in $filtering.scan_numbers + [${scan_number.from},${scan_number.to}] + #end for + " + #end if + + #for threshold_entry in $filtering.threshold_repeat + --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation" + #end for + + + #if $filtering.strip_it.value + --filter "stripIT" + #end if + + #if $filtering.filter_mz_windows.do_filter + --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" + #end if + + + #if $filtering.filter_ms_levels.do_filter + --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "default" + --filter "ETDFilter" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" + --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units" + #end if + + + #end if + + </command> + + <inputs> + <!-- BEGIN_VERSION_RAW --> + <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/> + <!-- END_VERSION_RAW --> + + <param name="output_type" type="select" label="Output Type"> + <option value="mzML">mzML (indexed)</option> + <option value="unindexed_mzML">mzML (unindexed)</option> + <option value="mzXML">mzXML (indexed)</option> + <option value="unindexed_mzXML">mzXML (unindexed)</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <conditional name="filtering"> + <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> + + + <conditional name="peak_picking"> + <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> + <option value="1">MS1 Only (1)</option> + <option value="2">MS2 Only (2)</option> + <option value="2-">MS2 and on (2-)</option> + <option value="1-">All Levels (1-)</option> + </param> + <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> + </when> + </conditional> + + <repeat name="threshold_repeat" title="Filter by Threshold"> + <conditional name="threshold"> + <param type="select" label="Specify threshold on" name="threshold_type" help=""> + <option value="count">Peak count</option> + <option value="count-after-ties">Peak count (after ties)</option> + <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z --> + <option value="bpi-relative">Percent of base peak intensity</option> + <option value="tic-relative">Percent of total ion current</option> + <option value="tic-fraction">Aggregate percent of total ion current</option> + </param> + <when value="count"> + <param type="integer" name="value" label="Number of peaks to keep" value="100" /> + </when> + <when value="count-after-ties"> + <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" /> + </when> + <when value="absolute"> + <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" /> + </when> + <when value="bpi-relative"> + <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2" + /> + </when> + <when value="tic-relative"> + <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2" + /> + </when> + <when value="tic-fraction"> + <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" /> + </when> + </conditional> + <param type="select" label="Keep" name="orientation"> + <option value="most-intense">Most intense peaks</option> + <option value="least-intense">Least intense peaks</option> + </param> + </repeat> + + + <param name="activation" type="select" label="Filter by Activation"> + <option value="false" selected="true">no</option> + <option value="ETD">ETD</option> + <option value="CID">CID</option> + <option value="SA">SA</option> + <option value="HCD">HCD</option> + </param> + + <repeat name="indices" title="Filter Scan Indices"> + <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> + </repeat> + + <repeat name="scan_numbers" title="Filter Scan Numbers"> + <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> + </repeat> + + <conditional name="filter_mz_windows"> + <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> + <when value="false" /> + <when value="true"> + <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> + <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> + </when> + </conditional> + + <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> + + <conditional name="filter_ms_levels"> + <param name="do_filter" type="boolean" label="Filter MS Levels" /> + <when value="false" /> + <when value="true"> + <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> + </when> + </conditional> + + <conditional name="etd_filtering"> + <param name="do_etd_filtering" type="select" label="ETD Filtering"> + <option value="none" selected="true">none</option> + <option value="default">yes (with default options)</option> + <option value="advanced">yes (show advanced options) </option> + </param> + <when value="none" /> + <when value="default" /> + <when value="advanced"> + <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> + </param> + <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> + <option value="MZ" selected="true">mz</option> + <option value="PPM">ppm</option> + </param> + <param name="remove_precursor" type="select" label="ETD Remove Precursor"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="blanket_removal" type="select" label="ETD Blanket Removal"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + </when> + </conditional> + + + </when> + </conditional> + + <conditional name="settings"> + <param name="settingsType" type="select" label="Advanced Settings" help=""> + <option value="default">Use Defaults</option> + <option value="full">Full Parameter List</option> + </param> + <when value="default" /> + <when value="full"> + <param type="select" name="binary_encoding" label="Binary Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="mz_encoding" label="m/z Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> + <option value="64">64</option> + <option value="32" selected="true">32</option> + </param> + <param type="boolean" name="zlib" label="Use zlib"> + </param> + </when> + </conditional> + + + </inputs> + <outputs> + <data format="mzml" name="output"> + <change_format> + <when input="output_type" value="mzXML" format="mzxml" /> + <when input="output_type" value="unindexed_mzXML" format="mzxml" /> + <when input="output_type" value="ms2" format="ms2" /> + <when input="output_type" value="mgf" format="mgf" /> + </change_format> + </data> + </outputs> + + <requirements> + <requirement type="package">proteowizard</requirement> + </requirements> + + <help> +**What it does** + +Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. + +You can view the original documentation here_. + +.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html + +------ + +**Citation** + +For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert3.xml Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,377 @@ +<tool id="msconvert3" name="msconvert3" version="0.1.0"> + <!-- BEGIN_VERSION_DEFAULT --> + <description>Convert and filter a mass spec peak list</description> + <!-- END_VERSION_DEFAULT --> + + <command interpreter="python"> + msconvert_wrapper.py + --input=${input} + #if hasattr($input, 'display_name') + --input_name='${input.display_name}' + #end if + --output=${output} + ## BEGIN_VERSION_DEFAULT + --fromextension=${input.ext} + ## END_VERSION_DEFAULT + + + --toextension=${output_type} + + #if $settings.settingsType == "full" + --binaryencoding=${settings.binary_encoding} + --mzencoding=${settings.mz_encoding} + --intensityencoding=${settings.intensity_encoding} + --zlib=${settings.zlib} + #end if + + #if $filtering.filtering_use + + #if $filtering.precursor_recalculation.value + --filter "precursorRecalculation" + #end if + + #if $filtering.peak_picking.pick_peaks + --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" + #end if + + #if str($filtering.activation) != "false" + --filter "activation $filtering.activation" + #end if + + #if len($filtering.indices) > 0 + --filter "index + #for $index in $filtering.indices + [${index.from},${index.to}] + #end for + " + #end if + + #if len($filtering.scan_numbers) > 0 + --filter "scanNumber + #for $scan_number in $filtering.scan_numbers + [${scan_number.from},${scan_number.to}] + #end for + " + #end if + + #for threshold_entry in $filtering.threshold_repeat + --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation" + #end for + + + #if $filtering.strip_it.value + --filter "stripIT" + #end if + + #if $filtering.filter_mz_windows.do_filter + --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" + #end if + + + #if $filtering.filter_ms_levels.do_filter + --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "default" + --filter "ETDFilter" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" + --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units" + #end if + + ## BEGIN_VERSION_3 + + #if $filtering.precursor_refine.value + --filter "precursorRefine" + #end if + + #if $filtering.ms2denoise.denoise + --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax" + #end if + + #if str($filtering.ms2deisotope) == "true" + --filter "MS2Deisotope" + #end if + + #if str($filtering.polarity) != "false" + --filter "polarity $filtering.polarity" + #end if + + #if str($filtering.analyzer) != "false" + --filter "analyzer $filtering.analyzer" + #end if + + ## END_VERSION_3 + + #end if + + </command> + + <inputs> + + <!-- BEGIN_VERSION_DEFAULT --> + <conditional name="type"> + <param name="input_type" type="select" label="Input Type"> + <option value="mzml">mzML</option> + <option value="mzxml">mzXML</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <when value="mzml"> + <param format="mzml" name="input" type="data" label="Input mzML"/> + </when> + <when value="mzxml"> + <param format="mzxml" name="input" type="data" label="Input mzXML"/> + </when> + <when value="mgf"> + <param format="mgf" name="input" type="data" label="Input mgf"/> + </when> + <when value="ms2"> + <param format="ms2" name="input" type="data" label="Input ms2"/> + </when> + </conditional> + <!-- END_VERSION_DEFAULT --> + <param name="output_type" type="select" label="Output Type"> + <option value="mzML">mzML (indexed)</option> + <option value="unindexed_mzML">mzML (unindexed)</option> + <option value="mzXML">mzXML (indexed)</option> + <option value="unindexed_mzXML">mzXML (unindexed)</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <conditional name="filtering"> + <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> + <!-- BEGIN_VERSION_3 --> + <param type="boolean" name="precursor_refine" label="Refine Precursor?" /> + <!-- END_VERSION_3 --> + + + <conditional name="peak_picking"> + <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> + <option value="1">MS1 Only (1)</option> + <option value="2">MS2 Only (2)</option> + <option value="2-">MS2 and on (2-)</option> + <option value="1-">All Levels (1-)</option> + </param> + <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> + </when> + </conditional> + + <repeat name="threshold_repeat" title="Filter by Threshold"> + <conditional name="threshold"> + <param type="select" label="Specify threshold on" name="threshold_type" help=""> + <option value="count">Peak count</option> + <option value="count-after-ties">Peak count (after ties)</option> + <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z --> + <option value="bpi-relative">Percent of base peak intensity</option> + <option value="tic-relative">Percent of total ion current</option> + <option value="tic-fraction">Aggregate percent of total ion current</option> + </param> + <when value="count"> + <param type="integer" name="value" label="Number of peaks to keep" value="100" /> + </when> + <when value="count-after-ties"> + <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" /> + </when> + <when value="absolute"> + <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" /> + </when> + <when value="bpi-relative"> + <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2" + /> + </when> + <when value="tic-relative"> + <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2" + /> + </when> + <when value="tic-fraction"> + <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" /> + </when> + </conditional> + <param type="select" label="Keep" name="orientation"> + <option value="most-intense">Most intense peaks</option> + <option value="least-intense">Least intense peaks</option> + </param> + </repeat> + + + <param name="activation" type="select" label="Filter by Activation"> + <option value="false" selected="true">no</option> + <option value="ETD">ETD</option> + <option value="CID">CID</option> + <option value="SA">SA</option> + <option value="HCD">HCD</option> + <!-- BEGIN_VERSION_3 --> + <option>BIRD</option> + <option>ECD</option> + <option>IRMPD</option> + <option>PD</option> + <option>PSD</option> + <option>PQD</option> + <option>SID</option> + <option>SORI</option> + <!-- END_VERSION_3 --> + </param> + + <repeat name="indices" title="Filter Scan Indices"> + <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> + </repeat> + + <repeat name="scan_numbers" title="Filter Scan Numbers"> + <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> + </repeat> + + <conditional name="filter_mz_windows"> + <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> + <when value="false" /> + <when value="true"> + <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> + <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> + </when> + </conditional> + + <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> + + <conditional name="filter_ms_levels"> + <param name="do_filter" type="boolean" label="Filter MS Levels" /> + <when value="false" /> + <when value="true"> + <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> + </when> + </conditional> + + <conditional name="etd_filtering"> + <param name="do_etd_filtering" type="select" label="ETD Filtering"> + <option value="none" selected="true">none</option> + <option value="default">yes (with default options)</option> + <option value="advanced">yes (show advanced options) </option> + </param> + <when value="none" /> + <when value="default" /> + <when value="advanced"> + <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> + </param> + <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> + <option value="MZ" selected="true">mz</option> + <option value="PPM">ppm</option> + </param> + <param name="remove_precursor" type="select" label="ETD Remove Precursor"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="blanket_removal" type="select" label="ETD Blanket Removal"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + </when> + </conditional> + + + <!-- BEGIN_VERSION_3 --> + <conditional name="ms2denoise"> + <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" /> + <when value="true"> + <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" /> + <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" /> + <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" /> + </when> + <when value="false" /> + </conditional> + <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" /> + + <param name="polarity" type="select" label="Filter by Polarity"> + <option value="false" selected="true">no</option> + <option value="positive">positive</option> + <option value="negative">negative</option> + </param> + + <param name="analyzer" type="select" label="Filter by Analyzer"> + <option value="false" selected="true">no</option> + <option value="quad">quad</option> + <option value="orbi">orbi</option> + <option value="FT">FT</option> + <option value="IT">IT</option> + <option value="TOF">TOF</option> + </param> + <!-- END_VERSION_3 --> + </when> + </conditional> + + <conditional name="settings"> + <param name="settingsType" type="select" label="Advanced Settings" help=""> + <option value="default">Use Defaults</option> + <option value="full">Full Parameter List</option> + </param> + <when value="default" /> + <when value="full"> + <param type="select" name="binary_encoding" label="Binary Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="mz_encoding" label="m/z Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> + <option value="64">64</option> + <option value="32" selected="true">32</option> + </param> + <param type="boolean" name="zlib" label="Use zlib"> + </param> + </when> + </conditional> + + + </inputs> + <outputs> + <data format="mzml" name="output"> + <change_format> + <when input="output_type" value="mzXML" format="mzxml" /> + <when input="output_type" value="unindexed_mzXML" format="mzxml" /> + <when input="output_type" value="ms2" format="ms2" /> + <when input="output_type" value="mgf" format="mgf" /> + </change_format> + </data> + </outputs> + + <requirements> + <requirement type="package">proteowizard</requirement> + </requirements> + + <help> +**What it does** + +Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. + +You can view the original documentation here_. + +.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html + +------ + +**Citation** + +For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert3_raw.xml Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,358 @@ +<tool id="msconvert3_raw" name="msconvert3_raw" version="0.1.0"> + <!-- BEGIN_VERSION_RAW --> + <description>Convert and filter a Thermo Finnigan RAW file</description> + <!-- END_VERSION_RAW --> + + <command interpreter="python"> + msconvert_wrapper.py + --input=${input} + #if hasattr($input, 'display_name') + --input_name='${input.display_name}' + #end if + --output=${output} + + ## BEGIN_VERSION_RAW + --fromextension=RAW + ## END_VERSION_RAW + + --toextension=${output_type} + + #if $settings.settingsType == "full" + --binaryencoding=${settings.binary_encoding} + --mzencoding=${settings.mz_encoding} + --intensityencoding=${settings.intensity_encoding} + --zlib=${settings.zlib} + #end if + + #if $filtering.filtering_use + + #if $filtering.precursor_recalculation.value + --filter "precursorRecalculation" + #end if + + #if $filtering.peak_picking.pick_peaks + --filter "peakPicking $filtering.peak_picking.prefer_vendor_peaks $filtering.peak_picking.ms_levels" + #end if + + #if str($filtering.activation) != "false" + --filter "activation $filtering.activation" + #end if + + #if len($filtering.indices) > 0 + --filter "index + #for $index in $filtering.indices + [${index.from},${index.to}] + #end for + " + #end if + + #if len($filtering.scan_numbers) > 0 + --filter "scanNumber + #for $scan_number in $filtering.scan_numbers + [${scan_number.from},${scan_number.to}] + #end for + " + #end if + + #for threshold_entry in $filtering.threshold_repeat + --filter "threshold $threshold_entry.threshold.threshold_type $threshold_entry.threshold.value $threshold_entry.orientation" + #end for + + + #if $filtering.strip_it.value + --filter "stripIT" + #end if + + #if $filtering.filter_mz_windows.do_filter + --filter "mzWindow [$filtering.filter_mz_windows.from,$filtering.filter_mz_windows.to]" + #end if + + + #if $filtering.filter_ms_levels.do_filter + --filter "msLevel [$filtering.filter_ms_levels.from, $filtering.filter_ms_levels.to]" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "default" + --filter "ETDFilter" + #end if + + #if str($filtering.etd_filtering.do_etd_filtering) == "advanced" + --filter "ETDFilter removePrecursor:$filtering.etd_filtering.remove_precursor removeChargeReduced:$filtering.etd_filtering.remove_charge_reduced removeNeutralLoss:$filtering.etd_filtering.remove_neutral_loss blanketRemoval:$filtering.etd_filtering.blanket_removal MatchingTolerance:$filtering.etd_filtering.matching_tolerance $filtering.etd_filtering.matching_tolerance_units" + #end if + + ## BEGIN_VERSION_3 + + #if $filtering.precursor_refine.value + --filter "precursorRefine" + #end if + + #if $filtering.ms2denoise.denoise + --filter "MS2Denoise $filtering.ms2denoise.num_peaks $filtering.ms2denoise.window_width $filtering.ms2denoise.relax" + #end if + + #if str($filtering.ms2deisotope) == "true" + --filter "MS2Deisotope" + #end if + + #if str($filtering.polarity) != "false" + --filter "polarity $filtering.polarity" + #end if + + #if str($filtering.analyzer) != "false" + --filter "analyzer $filtering.analyzer" + #end if + + ## END_VERSION_3 + + #end if + + </command> + + <inputs> + <!-- BEGIN_VERSION_RAW --> + <param format="RAW" name="input" type="data" label="Thermo Finnigan RAW Input"/> + <!-- END_VERSION_RAW --> + + <param name="output_type" type="select" label="Output Type"> + <option value="mzML">mzML (indexed)</option> + <option value="unindexed_mzML">mzML (unindexed)</option> + <option value="mzXML">mzXML (indexed)</option> + <option value="unindexed_mzXML">mzXML (unindexed)</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <conditional name="filtering"> + <param name="filtering_use" type="boolean" label="Use Filtering?" help="" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param type="boolean" name="precursor_recalculation" label="Recalculate Precursor?" /> + <!-- BEGIN_VERSION_3 --> + <param type="boolean" name="precursor_refine" label="Refine Precursor?" /> + <!-- END_VERSION_3 --> + + + <conditional name="peak_picking"> + <param type="boolean" name="pick_peaks" label="Use Peak Picking?" truevalue="true" falsevalue="false" /> + <when value="false" /> + <when value="true"> + <param name="ms_levels" type="select" label="Peak Peaking - Apply to MS Levels"> + <option value="1">MS1 Only (1)</option> + <option value="2">MS2 Only (2)</option> + <option value="2-">MS2 and on (2-)</option> + <option value="1-">All Levels (1-)</option> + </param> + <param type="boolean" name="prefer_vendor_peaks" label="Peak Picking - Prefer Vendor Peaks?" truevalue="true" falsevalue="false" checked="true"/> + </when> + </conditional> + + <repeat name="threshold_repeat" title="Filter by Threshold"> + <conditional name="threshold"> + <param type="select" label="Specify threshold on" name="threshold_type" help=""> + <option value="count">Peak count</option> + <option value="count-after-ties">Peak count (after ties)</option> + <option value="absolute">Peak absolute intensity</option><!-- TODO: absolute what? m/z --> + <option value="bpi-relative">Percent of base peak intensity</option> + <option value="tic-relative">Percent of total ion current</option> + <option value="tic-fraction">Aggregate percent of total ion current</option> + </param> + <when value="count"> + <param type="integer" name="value" label="Number of peaks to keep" value="100" /> + </when> + <when value="count-after-ties"> + <param type="integer" name="value" label="Number of peaks to keep (after ties)" value="100" /> + </when> + <when value="absolute"> + <param type="float" name="value" label="Absolute intensity cut-off" value="100.0" /> + </when> + <when value="bpi-relative"> + <param type="float" name="value" label="Keep peaks above (or below) this fraction of base peak intensity" value="0.2" + /> + </when> + <when value="tic-relative"> + <param type="float" name="value" label="Keep peaks above (or below) this fraction of total ion current" value="0.2" + /> + </when> + <when value="tic-fraction"> + <param type="float" name="value" label="Keep peaks until this fraction of total ion current is accounted for" value="0.8" /> + </when> + </conditional> + <param type="select" label="Keep" name="orientation"> + <option value="most-intense">Most intense peaks</option> + <option value="least-intense">Least intense peaks</option> + </param> + </repeat> + + + <param name="activation" type="select" label="Filter by Activation"> + <option value="false" selected="true">no</option> + <option value="ETD">ETD</option> + <option value="CID">CID</option> + <option value="SA">SA</option> + <option value="HCD">HCD</option> + <!-- BEGIN_VERSION_3 --> + <option>BIRD</option> + <option>ECD</option> + <option>IRMPD</option> + <option>PD</option> + <option>PSD</option> + <option>PQD</option> + <option>SID</option> + <option>SORI</option> + <!-- END_VERSION_3 --> + </param> + + <repeat name="indices" title="Filter Scan Indices"> + <param name="from" type="integer" label="Filter Scan Index From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter Scan Index To" value="0" optional="true" /> + </repeat> + + <repeat name="scan_numbers" title="Filter Scan Numbers"> + <param name="from" type="integer" label="Filter Scan Number From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter Scan Number To" value="0" optional="true" /> + </repeat> + + <conditional name="filter_mz_windows"> + <param name="do_filter" type="boolean" truevalue="true" falsevalue="false" label="Filter m/z Window" help="" /> + <when value="false" /> + <when value="true"> + <param name="from" type="float" label="Filter m/z From" value="0.0" optional="false" /> + <param name="to" type="float" label="Filter m/z To" value="0.0" optional="true" /> + </when> + </conditional> + + <param type="boolean" name="strip_it" label="Strip Ion Trap MS1 Scans" /> + + <conditional name="filter_ms_levels"> + <param name="do_filter" type="boolean" label="Filter MS Levels" /> + <when value="false" /> + <when value="true"> + <param name="from" type="integer" label="Filter MS Level From" value="0" optional="false" /> + <param name="to" type="integer" label="Filter MS Level To" value="0" optional="true" /> + </when> + </conditional> + + <conditional name="etd_filtering"> + <param name="do_etd_filtering" type="select" label="ETD Filtering"> + <option value="none" selected="true">none</option> + <option value="default">yes (with default options)</option> + <option value="advanced">yes (show advanced options) </option> + </param> + <when value="none" /> + <when value="default" /> + <when value="advanced"> + <param name="matching_tolerance" type="float" label="ETD Matching Tolernace" value="3.1"> + </param> + <param name="matching_tolerance_units" type="select" label="Units for ETD Matching Tolerance"> + <option value="MZ" selected="true">mz</option> + <option value="PPM">ppm</option> + </param> + <param name="remove_precursor" type="select" label="ETD Remove Precursor"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_charge_reduced" type="select" label="ETD Remove Charge Reduced"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="remove_neutral_loss" type="select" label="ETD Remove Neutral Loss"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + <param name="blanket_removal" type="select" label="ETD Blanket Removal"> + <option value="true" selected="true">yes</option> + <option value="false">no</option> + </param> + </when> + </conditional> + + + <!-- BEGIN_VERSION_3 --> + <conditional name="ms2denoise"> + <param name="denoise" type="boolean" label="De-noise MS2 with moving window filter" /> + <when value="true"> + <param name="num_peaks" label="De-noise: Number of peaks in window" value="6" type="integer" /> + <param name="window_width" type="float" label="De-noise: Window width (Daltons)" value="30" /> + <param name="relax" label="De-noise: Multicharge fragment relaxation" checked="true" type="boolean" truevalue="true" falsevalue="false" /> + </when> + <when value="false" /> + </conditional> + <param name="ms2deisotope" type="boolean" label="Deisotope MS2 using Markey method" help="" truevalue="true" falsevalue="false" /> + + <param name="polarity" type="select" label="Filter by Polarity"> + <option value="false" selected="true">no</option> + <option value="positive">positive</option> + <option value="negative">negative</option> + </param> + + <param name="analyzer" type="select" label="Filter by Analyzer"> + <option value="false" selected="true">no</option> + <option value="quad">quad</option> + <option value="orbi">orbi</option> + <option value="FT">FT</option> + <option value="IT">IT</option> + <option value="TOF">TOF</option> + </param> + <!-- END_VERSION_3 --> + </when> + </conditional> + + <conditional name="settings"> + <param name="settingsType" type="select" label="Advanced Settings" help=""> + <option value="default">Use Defaults</option> + <option value="full">Full Parameter List</option> + </param> + <when value="default" /> + <when value="full"> + <param type="select" name="binary_encoding" label="Binary Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="mz_encoding" label="m/z Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> + <option value="64">64</option> + <option value="32" selected="true">32</option> + </param> + <param type="boolean" name="zlib" label="Use zlib"> + </param> + </when> + </conditional> + + + </inputs> + <outputs> + <data format="mzml" name="output"> + <change_format> + <when input="output_type" value="mzXML" format="mzxml" /> + <when input="output_type" value="unindexed_mzXML" format="mzxml" /> + <when input="output_type" value="ms2" format="ms2" /> + <when input="output_type" value="mgf" format="mgf" /> + </change_format> + </data> + </outputs> + + <requirements> + <requirement type="package">proteowizard</requirement> + </requirements> + + <help> +**What it does** + +Converts between various mass spectrometry peak list representations. Additional options such as filtering and/or precursor recalculation are available. + +You can view the original documentation here_. + +.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html + +------ + +**Citation** + +For the underlying tool, please cite `ProteoWizard: Open Source Software for Rapid Proteomics Tools Development. Darren Kessner; Matt Chambers; Robert Burke; David Agus; Parag Mallick. Bioinformatics 2008; doi: 10.1093/bioinformatics/btn323.` + +If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-msconvert + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_raw_wrapper.py Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,124 @@ +#!/usr/bin/env python +import optparse +import os +import sys +import tempfile +import shutil +import subprocess +import re +from os.path import basename +import logging + +assert sys.version_info[:2] >= ( 2, 6 ) + +log = logging.getLogger(__name__) +working_directory = os.getcwd() +tmp_stderr_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stderr').name +tmp_stdout_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stdout').name + +def stop_err( msg ): + sys.stderr.write( "%s\n" % msg ) + sys.exit() + +def read_stderr(): + stderr = '' + if(os.path.exists(tmp_stderr_name)): + with open(tmp_stderr_name, 'rb') as tmp_stderr: + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read(buffsize) + if not stderr or len(stderr) % buffsize != 0: + break + except OverflowError: + pass + return stderr + +def execute(command, stdin=None): + with open(tmp_stderr_name, 'wb') as tmp_stderr: + with open(tmp_stdout_name, 'wb') as tmp_stdout: + proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) + returncode = proc.wait() + if returncode != 0: + raise Exception, "Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()) + +def delete_file(path): + if os.path.exists(path): + try: + os.remove(path) + except: + pass + +def delete_directory(directory): + if os.path.exists(directory): + try: + shutil.rmtree(directory) + except: + pass + +def symlink(source, link_name): + import platform + if platform.system() == 'Windows': + import win32file + win32file.CreateSymbolicLink(source, link_name, 1) + else: + os.symlink(source, link_name) + + +def copy_to_working_directory(data_file, relative_path): + if os.path.abspath(data_file) != os.path.abspath(relative_path): + shutil.copy(data_file, relative_path) + return relative_path + +def __main__(): + run_script() + +#ENDTEMPLATE + +to_extensions = ['mzML', 'mzXML', 'mgf', 'txt', 'ms2', 'cms2'] + +def str_to_bool(v): + """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """ + return v.lower() in ["yes", "true", "t", "1"] + + +def run_script(): + parser = optparse.OptionParser() + parser.add_option('--input', dest='input') + parser.add_option('--output', dest='output') + parser.add_option('--fromextension', dest='fromextension') + parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions) + parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64']) + parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64']) + parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64']) + parser.add_option('--noindex', dest='noindex') + parser.add_option('--zlib', dest='zlib') + parser.add_option('--filter', dest='filter', action='append', default=[]) + + (options, args) = parser.parse_args() + + filter_commands = '' + for filter in options.filter: + filter_commands = "%s --filter \"%s\"" % (filter_commands, filter) + + input_file = 'input.%s' % options.fromextension + copy_to_working_directory(options.input, input_file) + os.mkdir('output') + cmd = "msconvert --%s -o output" % (options.toextension) + if str_to_bool(options.noindex): + cmd = "%s %s" % (cmd, "--noindex") + if str_to_bool(options.zlib): + cmd = "%s %s" % (cmd, "--zlib") + cmd = "%s --%s" % (cmd, options.binaryencoding) + cmd = "%s --mz%s" % (cmd, options.mzencoding) + cmd = "%s --inten%s" % (cmd, options.intensityencoding) + cmd = "%s %s" % (cmd, input_file) + cmd = "%s %s" % (cmd, filter_commands) + print cmd + execute(cmd) + output_files = os.listdir('output') + assert len(output_files) == 1 + output_file = output_files[0] + shutil.copy(os.path.join('output', output_file), options.output) + +if __name__ == '__main__': __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_subset.xml Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,105 @@ +<tool id="msconvert_subset" name="Subset Peak List" version="0.1.0"> + <description>against list of scan numbers or indices.</description> + <command interpreter="python"> + msconvert_wrapper.py + --input=${input} + --output=${output} + --fromextension=${input.ext} + --toextension=${output_type} + #if $settings.settingsType == "full" + --binaryencoding=${settings.binary_encoding} + --mzencoding=${settings.mz_encoding} + --intensityencoding=${settings.intensity_encoding} + --zlib=${settings.zlib} + #end if + --filter_table="$filter.filterList" + #if $filter.filterType == "scan_number" + --filter_table_type="number" + #else + --filter_table_type="index" + #end if + </command> + + <inputs> + <conditional name="type"> + <param name="input_type" type="select" label="Input Type"> + <option value="mzml">mzML</option> + <option value="mzxml">mzXML</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <when value="mzml"> + <param format="mzml" name="input" type="data" label="Input mzML"/> + </when> + <when value="mzxml"> + <param format="mzxml" name="input" type="data" label="Input mzXML"/> + </when> + <when value="mgf"> + <param format="mgf" name="input" type="data" label="Input mgf"/> + </when> + <when value="ms2"> + <param format="ms2" name="input" type="data" label="Input ms2"/> + </when> + </conditional> + <param name="output_type" type="select" label="Output Type"> + <option value="mzML">mzML (indexed)</option> + <option value="unindexed_mzML">mzML (unindexed)</option> + <option value="mzXML">mzXML (indexed)</option> + <option value="unindexed_mzXML">mzXML (unindexed)</option> + <option value="mgf">mgf</option> + <option value="ms2">ms2</option> + </param> + <conditional name="filter"> + <param name="filterType" type="select" label="Filter by" help=""> + <option value="scan_number" selected="true">Scan Number</option> + <option value="scan_index">Scan Index</option> + </param> + <when value="scan_number"> + <param format="text" name="filterList" type="data" label="Scan Numbers"/> + </when> + <when value="scan_index"> + <param format="text" name="filterList" type="data" label="Scan Indices"/> + </when> + </conditional> + <conditional name="settings"> + <param name="settingsType" type="select" label="Advanced msconvert Settings" help=""> + <option value="default">Use Defaults</option> + <option value="full">Full Parameter List</option> + </param> + <when value="default" /> + <when value="full"> + <param type="select" name="binary_encoding" label="Binary Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="mz_encoding" label="m/z Encoding Precision"> + <option value="64" selected="true">64</option> + <option value="32">32</option> + </param> + <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32"> + <option value="64">64</option> + <option value="32" selected="true">32</option> + </param> + <param type="boolean" name="zlib" label="Use zlib"> + </param> + </when> + </conditional> + </inputs> + <outputs> + <data format="mzml" name="output"> + <change_format> + <when input="output_type" value="mzXML" format="mzxml" /> + <when input="output_type" value="unindexed_mzXML" format="mzxml" /> + <when input="output_type" value="ms2" format="ms2" /> + <when input="output_type" value="mgf" format="mgf" /> + </change_format> + </data> + </outputs> + + <requirements> + <requirement type="package">proteowizard</requirement> + </requirements> + + <help> + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/msconvert_wrapper.py Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,272 @@ +#!/usr/bin/env python +import optparse +import os +import sys +import tempfile +import shutil +import subprocess +import re +import logging + +assert sys.version_info[:2] >= (2, 6) + +log = logging.getLogger(__name__) +working_directory = os.getcwd() +tmp_stderr_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stderr').name +tmp_stdout_name = tempfile.NamedTemporaryFile(dir=working_directory, suffix='.stdout').name + + +def stop_err(msg): + sys.stderr.write("%s\n" % msg) + sys.exit() + + +def read_stderr(): + stderr = '' + if(os.path.exists(tmp_stderr_name)): + with open(tmp_stderr_name, 'rb') as tmp_stderr: + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read(buffsize) + if not stderr or len(stderr) % buffsize != 0: + break + except OverflowError: + pass + return stderr + + +def execute(command, stdin=None): + try: + with open(tmp_stderr_name, 'wb') as tmp_stderr: + with open(tmp_stdout_name, 'wb') as tmp_stdout: + proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ) + returncode = proc.wait() + if returncode != 0: + raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr())) + finally: + print open(tmp_stderr_name, "r").read() + print open(tmp_stdout_name, "r").read() + + +def delete_file(path): + if os.path.exists(path): + try: + os.remove(path) + except: + pass + + +def delete_directory(directory): + if os.path.exists(directory): + try: + shutil.rmtree(directory) + except: + pass + + +def symlink(source, link_name): + import platform + if platform.system() == 'Windows': + try: + import win32file + win32file.CreateSymbolicLink(source, link_name, 1) + except: + shutil.copy(source, link_name) + else: + os.symlink(source, link_name) + + +def copy_to_working_directory(data_file, relative_path): + if os.path.abspath(data_file) != os.path.abspath(relative_path): + symlink(data_file, relative_path) + return relative_path + + +def __main__(): + run_script() + +#ENDTEMPLATE + +to_extensions = ['mzML', 'mzXML', 'unindexed_mzML', 'unindexed_mzXML', 'mgf', 'txt', 'ms2', 'cms2'] + + +def str_to_bool(v): + """ From http://stackoverflow.com/questions/715417/converting-from-a-string-to-boolean-in-python """ + return v.lower() in ["yes", "true", "t", "1"] + + +def _add_filter(filters_file, contents): + filters_file.write("filter=%s\n" % contents) + + +def _skip_line(options, file_num, line_parts): + file_num_column = options.filter_table_file_column + if not file_num_column: + return False + else: + target_file_num_val = str(file_num).strip() + query_file_num_val = line_parts[int(file_num_column) - 1].strip() + #print "target %s, query %s" % (target_file_num_val, query_file_num_val) + return target_file_num_val != query_file_num_val + + +def _read_table_numbers(path, options, file_num=None): + unique_numbers = set([]) + column_num = options.filter_table_column + input = open(path, "r") + first_line = True + for line in input: + if not line: + continue + line = line.strip() + if line.startswith("#"): + first_line = False + continue + if column_num == None: + column = line + else: + line_parts = line.split("\t") + if _skip_line(options, file_num, line_parts): + continue + column = line_parts[int(column_num) - 1] + match = re.match("\d+", column) + if match: + unique_numbers.add(int(match.group())) + first_line = False + return unique_numbers + + +# TODO: Test on windows +def shellquote(s): + return "'" + s.replace("'", "'\\''") + "'" + + +def _add_filter_line_from_file(filter_file, options, file_num=None): + file = options.filter_table + if not file: + return + numbers = _read_table_numbers(file, options, file_num) + msconvert_int_set = " ".join([str(number) for number in numbers]) + filter_type = options.filter_table_type + if filter_type == 'number': + filter_prefix = 'scanNumber' + else: + filter_prefix = 'index' + _add_filter(filter_file, "%s %s" % (filter_prefix, msconvert_int_set)) + + +def _create_filters_file(options, file_num=None, debug=False): + suffix = "" if not file_num else str(file_num) + filters_file_path = "filters%s" % suffix + filters_file = open(filters_file_path, "w") + if options.filters_file: + filters_file.write(open(options.filters_file, "r").read()) + for filter in options.filter: + _add_filter(filters_file, filter) + _add_filter_line_from_file(filters_file, options, file_num=file_num) + + filters_file.close() + if debug: + print open(filters_file_path, "r").read() + return filters_file_path + + +def _build_base_cmd(options): + to_extension = options.toextension + if to_extension.startswith("unindexed_"): + to_extension = to_extension[len("unindexed_"):] + to_params = "--noindex" + else: + to_params = "" + cmd = "msconvert --%s %s" % (to_extension, to_params) + if str_to_bool(options.zlib): + cmd = "%s %s" % (cmd, "--zlib") + if options.binaryencoding: + cmd = "%s --%s" % (cmd, options.binaryencoding) + if options.mzencoding: + cmd = "%s --mz%s" % (cmd, options.mzencoding) + if options.intensityencoding: + cmd = "%s --inten%s" % (cmd, options.intensityencoding) + return cmd + + +def _run(base_cmd, output_dir='output', inputs=[], debug=False): + inputs_as_str = " ".join(['%s' % shellquote(input) for input in inputs]) + os.mkdir(output_dir) + cmd = "%s -o %s %s" % (base_cmd, shellquote(output_dir), inputs_as_str) + if debug: + print cmd + execute(cmd) + output_files = os.listdir(output_dir) + assert len(output_files) == 1 + output_file = output_files[0] + return os.path.join(output_dir, output_file) + + +def run_script(): + parser = optparse.OptionParser() + parser.add_option('--input', dest='inputs', action='append', default=[]) + parser.add_option('--input_name', dest='input_names', action='append', default=[]) + parser.add_option('--output', dest='output') + parser.add_option('--fromextension', dest='fromextension') + parser.add_option('--toextension', dest='toextension', default='mzML', choices=to_extensions) + parser.add_option('--binaryencoding', dest='binaryencoding', choices=['32', '64']) + parser.add_option('--mzencoding', dest='mzencoding', choices=['32', '64']) + parser.add_option('--intensityencoding', dest='intensityencoding', choices=['32', '64']) + parser.add_option('--zlib', dest='zlib', default="false") + parser.add_option('--filter', dest='filter', action='append', default=[]) + parser.add_option('--filters_file', dest='filters_file', default=None) + parser.add_option('--filter_table', default=None) + parser.add_option('--filter_table_type', default='index', choices=['index', 'number']) + parser.add_option('--filter_table_column', default=None) + parser.add_option('--filter_table_file_column', default=None) + parser.add_option('--debug', dest='debug', action='store_true', default=False) + + (options, args) = parser.parse_args() + if len(options.inputs) < 1: + stop_err("No input files to msconvert specified") + if len(options.input_names) > 0 and len(options.input_names) != len(options.inputs): + stop_err("Number(s) of supplied input names and input files do not match") + if not options.output: + stop_err("Must specify output location") + input_files = [] + for i, input in enumerate(options.inputs): + input_base = None + if len(options.input_names) > i: + input_base = options.input_names[i] + if not input_base: + input_base = 'input%s' % i + if not input_base.lower().endswith(options.fromextension.lower()): + input_file = '%s.%s' % (input_base, options.fromextension) + else: + input_file = input_base + input_file = input_file + copy_to_working_directory(input, input_file) + input_files.append(input_file) + + cmd = _build_base_cmd(options) + file_column = options.filter_table_file_column + if not file_column: + # Apply same filters to all files, just create a unviersal filter files + # and run msconvert once. + filters_file_path = _create_filters_file(options, debug=options.debug) + cmd = "%s -c %s" % (cmd, filters_file_path) + else: + # Dispatching on a column to filter different files differently, need to filter + # each input once with msconvert and then merge once. + filtered_files = [] + for index, input_file in enumerate(input_files): + filters_file_path = _create_filters_file(options, index + 1, debug=options.debug) + filter_cmd = "%s -c %s" % (cmd, filters_file_path) + filtered_output_file = _run(filter_cmd, output_dir='output%d' % index, inputs=[input_file], debug=options.debug) + filtered_files.append(filtered_output_file) + input_files = filtered_files + if len(input_files) > 1: + cmd = "%s --merge" % cmd + output_file = _run(cmd, output_dir='output', inputs=input_files, debug=options.debug) + shutil.copy(output_file, options.output) + + +if __name__ == '__main__': + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update.sh Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,35 @@ +#!/bin/bash + +LICENSE_FILE=LICENSE +# Ensure repository contains license file. +if [ ! -e "$LICENSE_FILE" ]; +then + wget http://www.apache.org/licenses/LICENSE-2.0.txt -O "$LICENSE_FILE" +fi + +# Run repository specific update actions. +if [ -f update_repo.sh ]; +then + ./update_repo.sh +fi + +wget https://raw.github.com/gist/3749747/README_GALAXYP.md -O README_GALAXYP.md + +# Create repository README +if [ ! -e README_REPO.md ]; +then + echo "TODO: Document this tool repository." > README_REPO.md +fi +cat README_REPO.md README_GALAXYP.md > README.md + + +# If version file exists, update all tools to this version +VERSION_FILE=version +if [ -e "$VERSION_FILE" ]; +then + VERSION=`cat $VERSION_FILE` + + # Replace tool version in each tool XML file ` + find -iname "*xml" -exec sed -i'' -e '0,/version="\(.\+\)"/s/version="\(.\+\)"/version="'$VERSION'"/1g' {} \; + +fi
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/update_repo.sh Wed Dec 19 00:10:08 2012 -0500 @@ -0,0 +1,9 @@ +#!/bin/bash + +sed -e '/BEGIN_VERSION_RAW/,/END_VERSION_RAW/d' -e '/BEGIN_VERSION_3/,/END_VERSION_3/d' -e 's/\$VERSION/2/g' -e 's/\$DESCRIPTION//g' msconvert.xml.template > msconvert2.xml +sed -e '/BEGIN_VERSION_DEFAULT/,/END_VERSION_DEFAULT/d' -e '/BEGIN_VERSION_3/,/END_VERSION_3/d' -e 's/\$VERSION/2/g' -e 's/\$DESCRIPTION/_raw/g' msconvert.xml.template > msconvert2_raw.xml + + +sed -e '/BEGIN_VERSION_RAW/,/END_VERSION_RAW/d' -e 's/\$VERSION/3/g' -e 's/\$DESCRIPTION//g' msconvert.xml.template > msconvert3.xml +sed -e '/BEGIN_VERSION_DEFAULT/,/END_VERSION_DEFAULT/d' -e 's/\$VERSION/3/g' -e 's/\$DESCRIPTION/_raw/g' msconvert.xml.template > msconvert3_raw.xml +